I. Introduction

I.1 Data origine (Mus musculus - tibialis anterior muscle)

In order to explore cell expression during muscle regeneration in young(2-3 months) and old(18-22 months) cells, RNAseq experiments were performed using cells sorted and FACs at four time points:

  • D0 muscles without injury
  • D2, 2 days after cardiotoxin-induced injury
  • D4, 4 days after injury
  • D7, 7 days after injury

The cell types sampled were as follows:

  • D0 , Endothelial Cells ECs, FibroAdipogenic Progenitors - FAPs, Muscle Stem Cells MuSCs.
  • D2 , ECs, FAPs, MuSCs., Neutrophile Cells, Inflammatory Macrophages - Inflammatory-Mac and Resolving Macrophages - Resolving-Mac .
  • D4, ECs, FAPs, MuSCs, Inflammatory-Mac, Resolving-Mac
  • D7, ECs, FAPs, MuSCs, Resolving-Mac

I.2 Pretreatment RNA-seq data with pipeline nfcore/rnaseq (v.1.4.2)

The RNA-seq data is aligned to the GRCm38 genome with STAR and counted with FeatureCount .

Only transcripts associated with coding proteins are kept.

Differentially expressed genes (DEG) processed with DESeq2_1.30.1 old vs young (reference expression is young one), for each cell type at each time Day_TypeCell_Old vs Day_TypeCell_Young

I.3 Differential Expression Genes Analysis

Report linksReportDEGanalysis

Report linksTableDEG

II Genes Set Enrichment Analysis (GSEA) results

GSEA on all genes. This analysis is done by day and cell type on list of genes ranked by logfoldchange sign * padj decreasing. The data base use is genes set from Molecular Signatures DataBase (MSigDB) species :

  • species = Mus musculus
  • category C2 = online pathway databases and the biomedical literature curated (more details )
  • subcategory = Canonical pathways ,Reactome database Composed by 1604 pathways.

II.1 Descriptives statistics

How many pathways are significants (padj<0.05)

ECs FAPs MuSCs Inflammatory-Mac Neutrophils Resolving-Mac NumberPathwayEnrichedByDay
D0 0 69 66 NA NA NA 103
D2 0 82 382 1 3 10 396
D4 125 4 284 2 NA 19 308
D7 4 0 17 NA NA 0 21
NumberPathwayEnrichedByTypeCell 126 108 466 3 3 29

II.2 Inspected Hierarchical Classement of pathway in REACTOME

All condition combined, there are 499 pathway enriched. In this representation only pathway with upper letter are enriched in at least one condition.

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II.3 Inspected the repartition of enrichied pathways across days and type cell

Number pathway
Numbers conditions enrichis 1 2 3 4 5 6 7 8
Numbers pathways 240 121 52 31 29 22 3 1

II.3.1 Pathways founds enriched in 8 conditions

II.3.2 Pathways founds enriched in 7 conditions

II.3.3 Pathways founds enriched in 6 conditions

II.3.4 Pathways founds enriched in 5 conditions

II.3.5 Pathways founds enriched in 4 conditions

Pathways founds enriched in 3 conditions

II.3.6 Pathways founds enriched in 2 conditions

II.3.7 Pathways founds enrichired in 1 condition

Table Recapitulatif